[BioC] ShortRead package

[Martin Morgan]

On 07/06/2012 10:10 AM, Fatemehsadat Seyednasrollah wrote:
> Hello every body
> I want to read a count read file with ShortRead package. When I make a AlignedRead object after reading the file, as the definition of object I have this line:
> class : AlignedRead
> length: 570000 reads, width : 36 cycles
>
> I want to know what does this "width" and "cycle" mean here?

Hi -- width is reporting the number of nucleotides in each read. In this 
case it says you've got reads that have resulted from 36 cycles of 
sequencing.  see also table(width(sread(aln))) for your AlignedRead 
object; also depending on what you want to do (e.g., counting reads in 
regions of interest) consider GenomicRanges::readGappedAlignments. The 
vignettes in various packages -- vignette(package="ShortRead"), 
vignette(package="GenomicRanges") -- can be helpful.

Martin

> thank you so much
> best regards,
> Narges
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